simplePheWAS:

# Defunct: the edits this existed to create are now part of the main package

# phenotype_manhattan <-
#   function(d, suggestive.line=0.05, significant.line,
#            OR.size=F,OR.direction=F,
#            annotate.level,
#            y.axis.interval=5,
#            y.axis.label=expression(-log[10](italic(p))),
#            max.y,
#            ...) {
#     if(sum(c("phenotype","p") %in% names(d))<2 ) stop("Data input must contain columns phenotype and p.")
#     if((OR.size|OR.direction)&!length(d$OR)) stop("OR size or direction requested, but d$OR not provided.")
#     #Check for size or direction parameter in addition to OR.size or OR.direction
#     if(OR.size & !is.null(list(...)$sizes)) stop("You cannot use OR.size=T for OR point sizes and use the second point sizing parameter 'sizes'.")
#     if(OR.direction & !is.null(list(...)$direction)) stop("You cannot use OR.direction=T for OR direction shapes and use the second point shape parameter 'direction'.")
#     #Check for renamed parameters
#     if(max(names(list(...)) %in% c("genomewide.line","sort.by.p","sort.by.category.p"))>0){
#       stop("'genomewide.line','sort.by.p', and 'sort.by.category.p' parameters have been replaced with 'significant.line','sort.by.value', and 'sort.by.category.value'")
#     }
#     #Remove records with NA p values
#     d=d[!is.na(d$p),]
#     #Transform the significance thresholds
#     if(missing(significant.line)) significant.line=suggestive.line/nrow(d)
#     significant.line=-log10(significant.line)
#     suggestive.line=-log10(suggestive.line)
#     if(missing(annotate.level)) {
#       if(is.na(significant.line)) {annotate.level=-log10(min(d$p,na.rm=T))}
#       else{annotate.level=significant.line}
#     }
#     else {annotate.level=-log10(annotate.level)}
#     #Nudge all of the p=0 results to the smallest double
#     if(sum(d$p==0)>0)d[d$p==0,]$p=.Machine$double.xmin
#     #Restrict to only those with appropriate p-values
#     d=d[d$p>0 & d$p<=1,]
#     
#     #Create the - log p value for plotting. No errors given restriction to p>0
#     d$value = -log10(d$p)
#     
#     max.y=ifelse(missing(max.y),max(ceiling(max(d$value)),4.4),max.y)
#     
#     #If OR sizes are requested, normalize them to magnitude only
#     #Commented: restrict to those reaching the annotation significance level
#     if(OR.size){
#       d$size = d$OR
#       d[d$size<1,]$size = 1/d[d$size<1,]$size
#       #d[d$value>=annotate.level,]$new.OR = 1
#     }
#     
#     #If the OR direction is requested, create it
#     if(OR.direction) d$direction = d$OR>=1
#     plot=phenotype_plot(d,suggestive.line=suggestive.line,significant.line=significant.line,
#                         sizes=OR.size,direction=OR.direction,
#                         annotate.level=annotate.level,
#                         y.axis.interval=y.axis.interval,
#                         y.axis.label=y.axis.label, max.y=max.y,title=d$snp,
#                         ...)
#     if(OR.size) plot=suppressWarnings(plot+scale_size("Odds Ratio", range = c(2, 4), breaks=c(1, 1.2, 1.6)))
#     plot
#   }